Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013887.1 Corchorus olitorius cultivar O-4 contig13920, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 20013
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30


Found at i:6913 original size:22 final size:22

Alignment explanation


    Indices: 6883--6954  Score: 62
    Period size: 22  Copynumber: 3.5  Consensus size: 22

       6873 ATTTTGGTCA

                *                 
       6883 TTATTGTTTATTTTTAGCATTT
          1 TTATAGTTTATTTTTAGCATTT

                         *  *   * 
       6905 TTATAGTTTA---GT-CCATCT
          1 TTATAGTTTATTTTTAGCATTT

              * *                 
       6923 TTGTTGTTTATTTTTAGCATTT
          1 TTATAGTTTATTTTTAGCATTT

                      
       6945 TTATAGTTTA
          1 TTATAGTTTA

       6955 GTCCATCTTT


Statistics
Matches: 35,  Mismatches: 11, Indels: 8
        0.65            0.20        0.15

Matches are distributed among these distances:
  18   12  0.34
  19    1  0.03
  21    1  0.03
  22   21  0.60

ACGTcount: A:0.19, C:0.07, G:0.11, T:0.62


Consensus pattern (22 bp):   
TTATAGTTTATTTTTAGCATTT

Found at i:6930 original size:40 final size:40

Alignment explanation


    Indices: 6886--6964  Score: 158
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       6876 TTGGTCATTA

                                                    
       6886 TTGTTTATTTTTAGCATTTTTATAGTTTAGTCCATCTTTG
          1 TTGTTTATTTTTAGCATTTTTATAGTTTAGTCCATCTTTG

                                                   
       6926 TTGTTTATTTTTAGCATTTTTATAGTTTAGTCCATCTTT
          1 TTGTTTATTTTTAGCATTTTTATAGTTTAGTCCATCTTT

       6965 CCCTTTTCCC


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   39  1.00

ACGTcount: A:0.18, C:0.10, G:0.11, T:0.61


Consensus pattern (40 bp):   
TTGTTTATTTTTAGCATTTTTATAGTTTAGTCCATCTTTG

Found at i:10629 original size:18 final size:18

Alignment explanation


    Indices: 10606--10640  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      10596 TAAAAAGGTT

                      *       
      10606 TTCAAAAATCCAAAAATA
          1 TTCAAAAATCAAAAAATA

                   *         
      10624 TTCAAAACTCAAAAAAT
          1 TTCAAAAATCAAAAAAT

      10641 CAAAAAAGAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23


Consensus pattern (18 bp):   
TTCAAAAATCAAAAAATA

Found at i:10721 original size:37 final size:37

Alignment explanation


    Indices: 10680--10765  Score: 118
    Period size: 37  Copynumber: 2.3  Consensus size: 37

      10670 TTCGAATCGA

                                  ***  *         
      10680 GAAAGTTCCCATCAAGTCTTCATGGTTTTCAAATTGG
          1 GAAAGTTCCCATCAAGTCTTCAAAATTGTCAAATTGG

                         *   *                   
      10717 GAAAGTTCCCATCCAGTTTTCAAAATTGTCAAATTGG
          1 GAAAGTTCCCATCAAGTCTTCAAAATTGTCAAATTGG

                        
      10754 GAAAGTTCCCAT
          1 GAAAGTTCCCAT

      10766 TAGTTTTCAA


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  37   43  1.00

ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Consensus pattern (37 bp):   
GAAAGTTCCCATCAAGTCTTCAAAATTGTCAAATTGG

Found at i:19873 original size:22 final size:22

Alignment explanation


    Indices: 19848--19892  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      19838 TAACATCTAA

                                  
      19848 TGATAATGATAAGTAATTTTGG
          1 TGATAATGATAAGTAATTTTGG

                                  
      19870 TGATAATGATAAGTAATTTTGG
          1 TGATAATGATAAGTAATTTTGG

             
      19892 T
          1 T

      19893 AACAATAAAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42


Consensus pattern (22 bp):   
TGATAATGATAAGTAATTTTGG
Done.